BBTools can de-interleave your file:

reformat.sh in=reads.fq out=r1.fq out2=r2.fq interleaved

Or you can just do your trimming with BBDuk instead, which accepts twin files or interleaved files:

bbduk.sh in=reads.fq out=trimmed.fq ref=adapters k=19 mink=9 ktrim=r hdist=1 tbo tpe interleaved

If your adapters are different than Illumina standard adapters you should to specify them. I've never worked with BGI data so I don't know. But, the "tbo" (trim by overlap) generally takes care of this anyway even if you don't know the adapter sequence. "tpe" (trim pairs evenly) is also a useful flag for adapter trimming because if adapter is detected at a certain position in one read, it should be at the same place in the paired read. I'm not aware of other adapter-trimming tools that offer these features; they allow more thorough trimming of paired files when processed together. I don't generally recommend processing your R1 and R2 files independently since that often results in disordered files or files with singletons, breaking the pairing.